Call them what you will, these Rebels were desperate to take the battle from the field to the streets.

A squad of hand-picked soldiers, dressed in civilian garb, gathers in secret to plot the destruction of a major city by fire. Another group attempts to derail an enemy train, with total disregard for the loss of life that would surely follow. A chemist plots the poisoning of a metropolitan reservoir, while a doctor—a man sworn to a life of healing—attempts to spread yellow fever throughout an entire nation.

These are not the acts of al-Qaida or any of a dozen other murderous extremist groups of the last 50 years. They were part of a well-financed, government-sponsored effort to stem—or at least delay—the inevitable defeat of the Confederacy. Were these merely guerrilla actions, justifiable under the rules of war, or were they indefensible acts of terrorism, perpetrated against non-combatants?

As the war was winding down—and looking increasingly dismal for the Confederacy—Jefferson Davis’ government hoped to foment an uprising of disenchanted Northerners, including Copperheads, members of the rabidly anti-Republican Order of American Knights and their subset, the Sons of Liberty. To this end, agents were sent to organize armed support in several of the North’s major cities. Northern men—unhappy with the war’s progress, dissatisfied with the Republican administration and sympathetic to the Southern cause—had promised to aid an ambitious plan to seize federal arsenals, liberate Northern prisoner-of-war camps and establish Rebel control of several Midwestern states. The idea was to sandwich the Union between two solid Confederate blocks, forcing it to submit. The plan was a longshot that never stood much chance of succeeding, but it was undermined by inertia, fear, corruption and betrayal.

The Confederates used their base in Canada to plan campaigns into the Union’s northernmost—and almost totally unprotected—flank. These lastditch, desperate operations were funded by Secretary of State Judah P. Benjamin to the tune of millions of dollars and approved by President Jefferson Davis. They were given nominal legitimacy by the formation, in late 1864, of the “Special and Secret Service Bureau.”

Some of the forays could be categorized as legitimate behind-the-lines military actions. Others were more problematic. While some raiders were fastidious in their attempts to preserve life, others deliberately set out to kill civilians, destroy property and leave devastation in their wake. “The authorities of the Confederate States appear…to have exhausted all possible efforts for humane and honorable warfare,” wrote Lieutenant John W. Headley, one of the leaders of Confederate secret operations in Canada. As the gloves came off, plots were hatched that to this day defy justification.

Dr. Luke Pryor Blackburn took, and apparently forgot, the Hippocratic Oath. An outwardly selfless healer, the soft-spoken Kentucky-born physician spent months in 1864 attending the sick during a raging yellow fever epidemic in Bermuda. Always gentle, ever soothing, he would hold his patients as they shivered, raved, bled, voided, vomited black bile and frequently died. The nurses and other doctors saw him as a saint—so much so that they didn’t question why the soiled bedding and clothes of his patients disappeared after Blackburn treated them. None imagined he was crating the filthy linens and shipping them to various Northern cities to cause a yellow fever epidemic that would cripple the Union. For good measure, he included some items infected by smallpox.

In all, eight trunks were sent north. Blackburn was especially proud of the trunk he dubbed “Big Number Two,” which he dispatched to Washington, D.C., bragging that it would “kill them at sixty yards distance.” Ultimately, the trunks proved harmless. It was not known at the time—and in fact unproven until 1900—that the disease is caused by the bite of infected mosquitoes, not through exposure to contaminated bed linens.

Unbeknown to his coworkers, Luke Blackburn— the kindhearted, portly, middle-aged friend to the suffering—had been a Con – federate “citizen agent” since the war began whose love for the South justified—in his own mind—a sojourn into bioterrorism. Blackburn knew there was no known cure for yellow fever, and that the mortality rate could reach as high as 50 percent. As one historian noted, “His knowledge of the psychological and physical devastation caused by the disease was obvious.”

Blackburn’s plot was discovered in April 1865, shortly after Robert E. Lee’s surrender and the assassination of President Abraham Lincoln. Newspapers called him the “Yellow Fever Fiend” and accused him of “one of the most fiendish plots ever concocted by the wickedness of man.”

He had traveled to Canada after leaving Bermuda, thinking himself safe there, but Canadian authorities took him into custody, indicted and tried him for violating Canada’s neutrality act. He was acquitted, and—knowing serious charges awaited him in his own country—remained in Canada until 1873. Homesick, and learning of a yellow fever epidemic afflicting the South, he ventured back to Kentucky and once again endeared himself as a savior of the sick—so much so that he was elected governor in 1879. He is remembered for his prison reforms—and for the first successful quarantine against the spread of yellow fever in the Mississippi River valley. If his brief career as a bioterrorist is recalled at all, it is generally dismissed as the rash act of an overzealous Southern patriot.

Shortly before Election Day in November 1864, eight Rebels— all veterans—gathered in New York City under the command of a hardcore Confederate colonel named Robert M. Martin. Martin was a friend of John Wilkes Booth, and would himself make an unsuccessful attempt on the life of President Lincoln the following March. At first, the plan called for saboteurs to set distraction fires to keep the public’s attention from the real Rebel objective—raiding the arsenal and occupying the city, with the help of what they believed would be an army of sympathizers. New York Governor Horatio Seymour, a Democrat and outspoken Lincoln critic, allegedly promised the state militia would not interfere with the plot, and everything seemed in readiness. As with nearly all the other secret Rebel plots, however, word of the plan leaked and thousands of Federal troops were sent to Gotham to thwart any enemy action.

Once it was clear there would be no grassroots rising to storm the city’s arsenal, the small squad of Confederates decided to go ahead with a modified version of the plan: They would burn New York City to the ground.

For these battle-hardened veterans, it wasn’t a huge leap. John Headley, a member of the team, later wrote that they were resolved in “our purpose to set the city on fire and give the people a scare if nothing else, and let the Government at Washington understand that burning homes in the South might find a counterpart in the North.” Martin later wrote that he saw “the way to bring the North to its senses was to burn Northern cities.”

A retired druggist had been secretly contracted to make 12 dozen four-ounce bottles of Greek fire, a liquid chemical concoction that had been in use for centuries. It burned instantly when exposed to air, spread wildly and was impervious to water. All it needed was oxygen. In the wrong hands, 144 bottles of this liquid devastation could cause untold damage.

Once they claimed their satchel of Greek fire, “we were now ready to create a sensation in New York,” Headley recalled. They would set fires in the various hotels, “so as to do the greatest damage in the business district on Broadway.” They agreed, however, to begin the operation at 8 p.m., to give the hotel guests the opportunity to escape, “as we did not want to destroy any lives.”

Either they were hopelessly naïve or Headley is dissembling. Given the war records of these young men—a number had ridden with the Confederate raider John Hunt Morgan and had escaped from Union prison camps—and their understanding that Greek fire “burned everything it touched,” they would have been delusional indeed not to anticipate a tremendous loss of life had they succeeded. One of the squad, Captain Robert Cobb Kennedy of the 1st Louisiana Infantry, later confessed, “I wish to say that…in retaliation for Sheridan’s atrocities in the Shenandoah Valley we desired to destroy property, not the lives of women and children although that would of course have followed in its train.” [emphasis added]

By the time they were ready, two of their number had fled. Each of the remaining men assigned himself four hotels, and carried 10 of the small bottles in his pockets. The idea was to start a fire in a hotel room, then immediately move on to the next target. Headley, walking from one hotel to the next, was surprised to see P.T. Barnum’s American Museum in flames. Kennedy had apparently downed a few drinks before starting out, and decided to improvise. There were 2,500 people attending a presentation in the museum’s lecture hall. Miraculously, no one was injured.

Despite setting small fires in 19 hotels and Barnum’s Museum—and igniting some barges at the docks—the would-be destroyers utterly failed. They didn’t realize the incendiary liquid needed air to burn. In their mis guided efforts to keep the fires secret until the flames were uncontrollable, they had closed the windows and doors of the hotel rooms; as it ate up the oxygen, the fire gradually subsided and went out. The saboteurs created a panic, but little actual damage. Ironically, the structure most affected was Barnum’s museum, since the incendiary was thrown and left to burn in an open space.

Eluding a massive and determined manhunt, the party made its way safely back to Canada by way of a train to Albany. Only one man was ever tried and punished for the attack on New York City. Captain Robert Kennedy, attempting to return to his home, was captured in Detroit and returned to New York for trial. Less than a month before Lee’s surrender, he was marched out of his cell in the Fort Lafayette military prison and hanged.

In early April 1865, a member of the Confederate Secret Service’s Torpedo Bureau left Richmond for Washington, D.C. His mission: Blow up the White House, with President Lincoln and his Cabinet inside. The idea was to plant mines beneath the building that would be detonated“over the jubilation of the crowd” when the president and his Cabinet members stood together to listen to a public serenade.

The saboteur was Thomas F. Harney, and he was ideally chosen. Harney was, in the words of one writer, an “explosives wizard.” A native of Pennsylvania, he had forsaken the North and fought for the Confederacy throughout the war. After being wounded, captured and exchanged, Harney was selected to be part of the elite Torpedo Bureau. Here he found his true calling, becoming an expert at exploding things. “Wherever Harney went,” historian William A. Tidwell writes, “the Yankees suffered casualties and loss of equipment from explosive devices—mines, subterra shells, hand grenades, and innocent-appearing devices that would blow up.”

The job of infiltrating Harney into Washington fell to the famed Confederate “Gray Ghost,” Colonel John Singleton Mosby. According to a Union military report, Harney “brought ordnance to Colonel Mosby and joined his command.” On April 10, however, as Mosby was moving toward Washington, he was engaged in a skirmish and Harney was captured. Two days later, he was incarcerated in Washington’s Old Capitol Prison, and the plot to blow up the president came to naught.

Various historians argue that John Wilkes Booth and his party were well acquainted with the Harney plan, and only after it failed did Booth elect to pursue the plot that resulted, just two days later, in President Lincoln’s death. If, in fact, the Confederate Secret Service were involved in the assassination plot, it would suggest that Secretary of State Benjamin—and logically, President Davis—were at least aware of the “project,” and at worst, behind it.

There were a number of other plots—some merely planned, others carried as far as the perpetrators could—designed to destabilize and terrify the North. Union shipping was a prime target of Rebel saboteurs— specifically the St. Louis docks, struck at least four times.

At the time of the attack on New York, two other measures were considered: blowing up the dam that contained Croton Reservoir, which supplied much of New York’s water, and the outright poisoning of the city’s water supply. And in early 1865, one respected chemist, a Northern defector and former Columbia University professor, actually developed a poison gas—anticipating the Germans’ mustard gas by 50 years. Jefferson Davis approved it, but the war ended before it could be used. There was no lack of plots—only a shortage of time, opportunity and expertise to carry them out.

The men who deliberately set out to wreak havoc on a noncombatant civilian population through fire, poison, disease and assassination justified these plots partly as payback for the destruction rained upon the South. The devastation to Southern cities and much of the countryside was as complete as if they’d been the targets of saturation bombing—with the same degree of hopelessness and desperation that accompanies it. The North, for the most part, was spared, and emerged from the conflict with little visceral sense of the massive damage inflicted on the lower half of the country. Shortly before his execution, Captain Kennedy wrote in his confession, “We wanted to let the people of the North understand that there are two sides to this war, and they can’t be rolling in wealth and comfort while we in the South are bearing all the hardships and privations.”

Perhaps some of these men were seeking the renown that comes with perpetrating a desperate act with far-reaching ramifications. No one was more surprised than John Wilkes Booth when—hungry, exhausted, lamed and in agony—he discovered the public saw him not as a savior, but as a skulking murderer.

And in part, they attempted these desperate campaigns as a means of diverting Union troops from the battlefield, thereby providing the Confederacy with a desperate, last-ditch shot at military victory. Many of the plotters were young combat veterans—well educated, from good families and sincerely motivated by what they considered a righteous cause.

Because we romanticize the past, it is tempting to categorize the plotters simply as partisans and freedom fighters. But for a better understanding of this darker corner of our national conflict, we must examine their actions as objectively as possible, and in the harsh and unwavering light of current events.

Ron Soodalter is a columnist for America’s Civil War.

Originally published in the May 2010 issue of America’s Civil War. To subscribe, click here.

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